Amber Archive Apr 2003: by author

A. Hungie
- velocity auto-correlation function (Wed Apr 16 2003 - 09:25:32 PDT)
- Re: Unit of velocity (Thu Apr 03 2003 - 09:46:18 PST)
- Unit of velocity (Thu Apr 03 2003 - 05:38:59 PST)
Andreas Svrcek-Seiler
- Re: Protein - DNA complex simulation - protocol (Tue Apr 29 2003 - 01:50:22 PDT)
Bengt Svensson
- Amber on Parallel Sun? (Mon Apr 28 2003 - 14:59:14 PDT)
Bill Ross
- Re: question about H-bond in carnal? (Fri Apr 25 2003 - 11:57:20 PDT)
cailliez
- quasih (Thu Apr 17 2003 - 08:35:26 PDT)
caldwell.heimdal.compchem.ucsf.edu
- Re: topology file in large systems (Thu Apr 17 2003 - 15:25:49 PDT)
- Re: CYS and HIS (Wed Apr 16 2003 - 07:55:55 PDT)
- Re: SSBonds and charge problems (Fri Apr 11 2003 - 12:50:04 PDT)
Carlos P. Sosa
- Organic solvents (Thu Apr 17 2003 - 08:17:54 PDT)
- Re: Examples for Energy Minimisation methods (Tue Apr 01 2003 - 10:08:27 PST)
Carlos Simmerling
- Re: about molecular dynamics (Tue Apr 29 2003 - 20:30:06 PDT)
- Re: about molecular dynamics (Tue Apr 29 2003 - 18:14:39 PDT)
- anyone have AMBER benchmarks with gigabit ethernet? (Wed Apr 23 2003 - 11:37:07 PDT)
- Re: MD went crazy (Fri Apr 18 2003 - 12:04:49 PDT)
- Re: MD went crazy (Fri Apr 18 2003 - 10:31:41 PDT)
- Re: MD went crazy (Fri Apr 18 2003 - 09:17:11 PDT)
- Re: MD went crazy (Fri Apr 18 2003 - 08:20:07 PDT)
- Re: CCL:MPI run problem (Wed Apr 16 2003 - 13:26:42 PDT)
- Re: addles (Mon Apr 14 2003 - 09:22:29 PDT)
- Re: A problem in Sander production dynamics (Mon Apr 14 2003 - 04:21:04 PDT)
- Re: Using MPI, PBS (Wed Apr 02 2003 - 11:29:41 PST)
Carolina Salvador-Morales
- (no subject) (Mon Apr 07 2003 - 06:22:27 PDT)
chandran karunakaran
- AMBER (Sun Apr 20 2003 - 18:13:32 PDT)
- Re: AMBER (Tue Apr 15 2003 - 18:25:08 PDT)
- AMBER (Tue Apr 15 2003 - 16:55:16 PDT)
- Metalloprotein (Mon Apr 14 2003 - 18:18:39 PDT)
- Re: Tleap-metalloprotein (Thu Apr 10 2003 - 18:20:40 PDT)
- Tleap (Tue Apr 08 2003 - 16:01:21 PDT)
- Nitro group introduction in tyrosine residue (Mon Apr 07 2003 - 12:23:33 PDT)
Christoph Kluck
- force field parameters for phosphoserine (Tue Apr 29 2003 - 07:07:59 PDT)
Craig A Bayse
- mutating residues (Tue Apr 08 2003 - 09:09:38 PDT)
CUI, Guanglei
- Re: job stopped (Thu Apr 24 2003 - 13:32:29 PDT)
- Re: job stopped (Thu Apr 24 2003 - 11:06:25 PDT)
- Re: AMBER (Tue Apr 15 2003 - 17:32:12 PDT)
- Re: Proper Restraint usage (Tue Apr 15 2003 - 14:30:22 PDT)
- Re: very important (Tue Apr 08 2003 - 07:47:55 PDT)
Dat H. Nguyen
- Periodic Boundary Condition in AMBER7 (the sander module)! (Tue Apr 08 2003 - 14:44:37 PDT)
David A. Case
- Re: problem_namelist_reading (Tue Apr 29 2003 - 08:12:01 PDT)
- Re: force field parameters for phosphoserine (Tue Apr 29 2003 - 07:56:48 PDT)
- Re: how to restrain base pair (Mon Apr 28 2003 - 12:14:49 PDT)
- Re: non bonded pair list (Thu Apr 24 2003 - 16:24:37 PDT)
- Re: Annealing blown up (Thu Apr 24 2003 - 16:21:53 PDT)
- Re: Question: Nmode with counter ions. (Thu Apr 24 2003 - 16:16:22 PDT)
- Re: Problem_to_open_PROTON_INFO_file (Thu Apr 24 2003 - 08:30:32 PDT)
- Re: How to use GLYCAM force field in AMBER (Wed Apr 23 2003 - 14:51:30 PDT)
- Re: GB/SA (Wed Apr 23 2003 - 12:36:56 PDT)
- Re: makeDIST_RST (Thu Apr 17 2003 - 09:50:14 PDT)
- Re: AMBER (Tue Apr 15 2003 - 17:38:59 PDT)
- Re: ibelly and ntr (Tue Apr 15 2003 - 16:13:11 PDT)
- Re: Proper Restraint usage (Tue Apr 15 2003 - 14:04:50 PDT)
- Re: A problem in opening the file (Mon Apr 14 2003 - 23:50:04 PDT)
- Re: diffusion coefficients (Sun Apr 13 2003 - 23:03:15 PDT)
- Re: SSBonds and charge problems (Fri Apr 11 2003 - 22:29:53 PDT)
- Re: free energy in sander (Thu Apr 10 2003 - 15:45:05 PDT)
- Re: Groups defenition (Wed Apr 09 2003 - 08:59:11 PDT)
- Re: Tleap (Tue Apr 08 2003 - 18:09:46 PDT)
- Re: Periodic Boundary Condition in AMBER7 (the sander module)! (Tue Apr 08 2003 - 15:25:53 PDT)
- Re: problem with tleap (Tue Apr 08 2003 - 09:12:34 PDT)
- Re: protonate (Tue Apr 08 2003 - 09:06:21 PDT)
- Re: please kindly help (Mon Apr 07 2003 - 08:34:21 PDT)
- Re: sander & prmtop file generated from antechamber input ? (Sun Apr 06 2003 - 22:28:58 PDT)
- Re: Hydrogen bond energy (Thu Apr 03 2003 - 09:26:04 PST)
- Re: AMBER pdb help - lost atoms - Part 2 (Thu Apr 03 2003 - 09:23:41 PST)
- Re: Unit of velocity (Thu Apr 03 2003 - 09:18:11 PST)
- Re: A weird antechamber error (Wed Apr 02 2003 - 07:24:12 PST)
- Re: AMBER pdb help - lost atoms (Tue Apr 01 2003 - 18:17:41 PST)
- Re: Polarizable simulation2 (Tue Apr 01 2003 - 13:49:39 PST)
- Re: size of a simulation system (Tue Apr 01 2003 - 13:44:14 PST)
- Re: AMBER pdb help - lost atoms (Tue Apr 01 2003 - 12:19:35 PST)
David Cowburn
- Future of Structural Biology Conference, 2003, http://futurestructuralbiology.org (Tue Apr 29 2003 - 13:04:27 PDT)
- Future of structural biology conference (Thu Apr 24 2003 - 11:58:23 PDT)
Derek Smith
- Problem Finishing Tutorial (Mon Apr 21 2003 - 16:31:00 PDT)
dicksmit.umich.edu
- frcmod file for Free energy perturbation tutorial of valine to alanine (Fri Apr 04 2003 - 10:06:37 PST)
- (no subject) (Wed Apr 02 2003 - 11:32:37 PST)
Dr. Carter, President
- To: amber as a Nicer Person (Mon Apr 14 2003 - 01:16:06 PDT)
Dr.K.Veluraja
- Hydrogen bond energy (Thu Apr 03 2003 - 02:37:02 PST)
Dr.Rajendra Joshi
- test (Mon Apr 28 2003 - 18:58:57 PDT)
Filip Ryj�cek
- old prmtop format in AMBER 6 differs from what is presented in AMBER 7 manual (Wed Apr 02 2003 - 04:29:07 PST)
Florian Barth
- Re: ambpdb (Wed Apr 16 2003 - 04:59:42 PDT)
Francesc Corcho
- Bugfixes (Fri Apr 11 2003 - 04:40:08 PDT)
- RE: Amber7 and mpirun on Linux (Fri Apr 11 2003 - 04:28:32 PDT)
Francisco Blanco
- ambpdb and protonate in AMBER7 (Thu Apr 17 2003 - 04:38:29 PDT)
FyD
- Re: Description of ATOM type in GLYCAM (Tue Apr 29 2003 - 14:07:35 PDT)
- mm_pbsa & nmode (Tue Apr 08 2003 - 08:04:38 PDT)
Guanglei Cui
- Re: phi and psi angles analysis (Tue Apr 29 2003 - 20:31:11 PDT)
GUILLERMINA L ESTIU
- topology file in large systems (Thu Apr 17 2003 - 14:58:35 PDT)
Hai-Long Wang
- carnal hbond (Wed Apr 30 2003 - 11:03:39 PDT)
- anal question (Thu Apr 03 2003 - 13:48:11 PST)
Harikrishnan
- Re: Protein - DNA complex simulation - protocol (Tue Apr 29 2003 - 06:16:25 PDT)
- Re: any one has references to parallelization aspects of AMBER (Tue Apr 29 2003 - 04:54:51 PDT)
- Protein - DNA complex simulation - protocol (Mon Apr 28 2003 - 21:40:39 PDT)
Holger Gohlke
- Re: phi and psi angles analysis (Tue Apr 29 2003 - 16:48:50 PDT)
- Re: nmode and mm_pbsa questions? (Fri Apr 25 2003 - 15:21:05 PDT)
- Re: mm_pbsa nmode calculation (Wed Apr 23 2003 - 12:12:51 PDT)
- Re: question about MM-PBSA? (Thu Apr 17 2003 - 18:31:31 PDT)
- Re: No statistical output for MM-PBSA? (Wed Apr 16 2003 - 11:05:38 PDT)
- Re: ALA-scan problem with mm_pbsa.pl (Wed Apr 16 2003 - 10:40:44 PDT)
- Re: Side-chain/main-chain decomposition in MM-GBSA (Thu Apr 03 2003 - 14:46:52 PST)
Ioana Cozmuta
- Re: Problem Finishing Tutorial (Mon Apr 21 2003 - 16:41:13 PDT)
- characteristics of nucleic acids homopolymers (Tue Apr 08 2003 - 11:33:03 PDT)
- Re: Using MPI, PBS (Wed Apr 02 2003 - 11:13:01 PST)
- Re: size of a simulation system (Wed Apr 02 2003 - 10:37:40 PST)
- Re: AMBER pdb help - lost atoms (Tue Apr 01 2003 - 14:21:46 PST)
Jake Isaacs
- converting amber to gromos format (Wed Apr 23 2003 - 06:59:19 PDT)
Javier Cuervo
- MM-GBSA question (Fri Apr 18 2003 - 13:39:23 PDT)
- Groups defenition (Tue Apr 08 2003 - 13:31:27 PDT)
Jean-François Taly
- non bonded pair list (Thu Apr 24 2003 - 09:22:08 PDT)
John Bushnell
- Re: Request for Amber7 (xleap problem) (Tue Apr 22 2003 - 15:30:41 PDT)
Jones, Garth A
- SANDER Source Code Documentation (Thu Apr 10 2003 - 00:07:13 PDT)
Jose Ramon Blas
- Re: Organic Solvents (Tue Apr 22 2003 - 15:00:58 PDT)
Joseph Fernandez
- Re: free energy in sander (Thu Apr 10 2003 - 19:58:30 PDT)
- free energy in sander (Thu Apr 10 2003 - 14:32:52 PDT)
- free energy calculations (Fri Apr 04 2003 - 13:18:25 PST)
Karl N. Kirschner
- Adding ACE to chopped protein (Wed Apr 16 2003 - 13:08:45 PDT)
kbyun.wesleyan.edu
- Re: mm_pbsa nmode calculation (Wed Apr 23 2003 - 13:33:55 PDT)
- mm_pbsa nmode calculation (Wed Apr 23 2003 - 11:33:17 PDT)
- mm_pbsa_statistics.pm (Tue Apr 22 2003 - 09:40:10 PDT)
Khanh.Dao.iac.uib.no
- Re: problem_namelist_reading (Tue Apr 29 2003 - 22:26:58 PDT)
- problem_namelist_reading (Mon Apr 28 2003 - 23:19:46 PDT)
- Problem_to_open_PROTON_INFO_file (Thu Apr 24 2003 - 01:46:10 PDT)
- (no subject) (Mon Apr 21 2003 - 09:35:02 PDT)
- PME box information (Tue Apr 15 2003 - 02:56:38 PDT)
- Re: A problem in opening the file (Tue Apr 15 2003 - 00:19:58 PDT)
- A problem in opening the file (Mon Apr 14 2003 - 22:01:11 PDT)
Kristina Furse
- RE: ibelly and ntr (Wed Apr 16 2003 - 12:51:43 PDT)
- RE: size of a simulation system (Tue Apr 01 2003 - 14:36:01 PST)
kxg2248.njit.edu
- Re: AMBER pdb help - lost atoms - Part 2 (Thu Apr 03 2003 - 09:50:29 PST)
- AMBER pdb help - lost atoms (Tue Apr 01 2003 - 11:39:27 PST)
Lepsa
- Re: question about MM-PBSA? (Mon Apr 21 2003 - 23:50:42 PDT)
- Side-chain/main-chain decomposition in MM-GBSA (Thu Apr 03 2003 - 00:24:35 PST)
- Polarizable simulation2 (Tue Apr 01 2003 - 04:25:22 PST)
Ling Zhang
- The error in the trajectory file (Tue Apr 08 2003 - 09:37:58 PDT)
Lishan Yao
- Re: question about H-bond in carnal? (Sun Apr 27 2003 - 17:37:13 PDT)
- Re: question about H-bond in carnal? (Fri Apr 25 2003 - 08:24:56 PDT)
- question about H-bond in carnal? (Fri Apr 25 2003 - 07:44:55 PDT)
- Re: question about MM-PBSA? (Fri Apr 18 2003 - 07:10:24 PDT)
- question about MM-PBSA? (Thu Apr 17 2003 - 12:15:38 PDT)
- No statistical output for MM-PBSA? (Tue Apr 15 2003 - 19:25:22 PDT)
- question about MM-PBSA? (Tue Apr 08 2003 - 10:21:20 PDT)
Luis Gracia
- Re: ambpdb (Tue Apr 15 2003 - 21:40:57 PDT)
M. L. Dodson
- Re: trouble with OFF files (Mon Apr 21 2003 - 13:13:24 PDT)
Mac Brown
- trouble with OFF files (Mon Apr 21 2003 - 12:07:32 PDT)
- solvents aren't loading (Tue Apr 15 2003 - 13:20:15 PDT)
Masaki Tomimoto
- Question: Nmode with counter ions. (Thu Apr 24 2003 - 10:09:02 PDT)
McAteer, Kathleen
- Residual dipolar couplings (Wed Apr 30 2003 - 10:56:34 PDT)
Michael Crowley
- Re: MD went crazy (Fri Apr 18 2003 - 10:30:53 PDT)
Miguel de Federico
- Usubscribe (Fri Apr 11 2003 - 01:17:04 PDT)
Natasja Brooijmans
- Re: job stopped (Thu Apr 24 2003 - 11:55:06 PDT)
- Re: ALA-scan problem with mm_pbsa.pl (Wed Apr 16 2003 - 11:14:55 PDT)
- ALA-scan problem with mm_pbsa.pl (Sun Apr 13 2003 - 15:21:03 PDT)
- Re: Bugfixes (Fri Apr 11 2003 - 09:49:59 PDT)
Nick Polfer
- Annealing blown up (Thu Apr 24 2003 - 12:02:38 PDT)
Peng Tao
- Description of ATOM type in GLYCAM (Tue Apr 29 2003 - 12:14:52 PDT)
- How to use GLYCAM force field in AMBER (Tue Apr 22 2003 - 08:08:06 PDT)
Petrodler.aol.com
- Organic Solvents (Tue Apr 22 2003 - 03:57:11 PDT)
Pratul Agarwal
- Re: Protein - DNA complex simulation - protocol (Tue Apr 29 2003 - 07:39:18 PDT)
- Re: size of a simulation system (Wed Apr 02 2003 - 12:02:29 PST)
- Re: size of a simulation system (Wed Apr 02 2003 - 06:32:44 PST)
Rajendra P. OJHA
- Re: Fwd: Re: Request for Amber7 (fwd) (Tue Apr 22 2003 - 02:53:12 PDT)
Robert G. Endres
- Re: GB/SA (Wed Apr 30 2003 - 12:57:31 PDT)
- Re: GB/SA (Mon Apr 28 2003 - 11:10:56 PDT)
- GB/SA (Wed Apr 23 2003 - 09:26:14 PDT)
- growing side chains (Mon Apr 07 2003 - 11:37:30 PDT)
Roberto Gomperts
- New Machine.sgi_mpi file (Thu Apr 03 2003 - 10:33:35 PST)
ronnie
- about molecular dynamics (Tue Apr 29 2003 - 18:09:25 PDT)
Ross Walker
- RE: anyone have AMBER benchmarks with gigabit ethernet? (Thu Apr 24 2003 - 06:20:07 PDT)
- RE: anyone have AMBER benchmarks with gigabit ethernet? (Thu Apr 24 2003 - 02:42:57 PDT)
S.Swaminathan
- problem with tleap (Tue Apr 08 2003 - 18:56:44 PDT)
- protonate (Tue Apr 08 2003 - 12:14:50 PDT)
- please kindly help (Mon Apr 07 2003 - 19:03:34 PDT)
- general minimisation methods (Fri Apr 04 2003 - 16:26:48 PST)
- Examples for Energy Minimisation methods (Tue Apr 01 2003 - 12:35:41 PST)
Samy Name_removed_after_user_request
- addles (Tue Apr 08 2003 - 09:56:44 PDT)
Sanjeev B.S.
- Re: question about H-bond in carnal? (Mon Apr 28 2003 - 23:59:15 PDT)
- Re: question about H-bond in carnal? (Fri Apr 25 2003 - 08:53:35 PDT)
- Re: question about H-bond in carnal? (Fri Apr 25 2003 - 08:35:58 PDT)
Satish Kumar
- any one has references to parallelization aspects of AMBER (Tue Apr 29 2003 - 02:59:05 PDT)
Scott Brozell
- Re: debug leap (Sat Apr 19 2003 - 16:40:03 PDT)
- RE: Amber7 and mpirun on Linux (Fri Apr 11 2003 - 12:40:38 PDT)
- Re: Amber7 and mpirun on Linux (Thu Apr 10 2003 - 12:28:00 PDT)
Shafinaz
- very important (Tue Apr 08 2003 - 07:19:18 PDT)
- Trouble with AMBER 7 (Mon Apr 07 2003 - 13:59:52 PDT)
Shuang Ding
- how to restrain base pair (Mon Apr 28 2003 - 11:59:58 PDT)
Sichun Yang
- Trying to understand parm99.dat (Tue Apr 08 2003 - 17:44:32 PDT)
Soonmin Jang
- About electrostatic force calculations (Tue Apr 01 2003 - 21:58:38 PST)
Sophia Kondratova
- ptraj problem (Fri Apr 04 2003 - 06:00:46 PST)
Steve Seibold
- Proper Restraint usage (Tue Apr 15 2003 - 13:42:59 PDT)
- SSBonds and charge problems (Fri Apr 11 2003 - 12:54:23 PDT)
sychen
- Re: ibelly and ntr (Tue Apr 15 2003 - 20:03:57 PDT)
- Re: sander & prmtop file generated from antechamber input ? (Sun Apr 06 2003 - 09:12:44 PDT)
- Re: Problem of Hbond in CARNAL (Tue Apr 01 2003 - 06:23:11 PST)
Thomas Cheatham
- Re: diffusion coefficients (Mon Apr 14 2003 - 14:34:39 PDT)
- Re: A problem in Sander production dynamics (Mon Apr 14 2003 - 14:24:31 PDT)
Troy Wymore
- PSC Summer Workshop: Modeling from Protein Sequence to Structure (Thu Apr 24 2003 - 10:33:39 PDT)
Venkata S Koppuravuri
- Re: Problem_to_open_PROTON_INFO_file (Thu Apr 24 2003 - 12:43:59 PDT)
- Re: ambpdb (Fri Apr 18 2003 - 09:14:34 PDT)
- Using MPI, PBS (Wed Apr 02 2003 - 10:58:23 PST)
Viktor Hornak
- Re: Amber on Linux (Sat Apr 12 2003 - 16:41:41 PDT)
Vlad
- Beyond 1,000,000 atoms (Wed Apr 02 2003 - 14:45:21 PST)
vze6jslz.verizon.net
- debug leap (Sat Apr 19 2003 - 11:52:40 PDT)
Wayne Dawson
- troubles on RS6000 (Mon Apr 28 2003 - 02:37:50 PDT)
Wen Li
- Re: Amber on Linux (Sun Apr 13 2003 - 08:06:52 PDT)
- Amber on Linux (Sat Apr 12 2003 - 10:00:46 PDT)
- Amber7 and mpirun on Linux (Thu Apr 10 2003 - 11:14:59 PDT)
- frcmod file (Thu Apr 03 2003 - 12:04:34 PST)
- size of a simulation system (Tue Apr 01 2003 - 07:49:42 PST)
wentaofu
- nmode and mm_pbsa questions? (Fri Apr 25 2003 - 13:47:48 PDT)
- nmode for S calculation (Tue Apr 08 2003 - 16:22:47 PDT)
William Wei
- MPI run problem (Wed Apr 16 2003 - 09:36:31 PDT)
- a-Helix direction? (Mon Apr 07 2003 - 13:26:40 PDT)
Xiao Jian Tan
- phi and psi angles analysis (Tue Apr 29 2003 - 16:27:17 PDT)
Xiaoqin Huang
- unsubscribe from the mail list (Thu Apr 17 2003 - 05:15:11 PDT)
Yong Duan
- RE: diffusion coefficients (Sun Apr 13 2003 - 20:50:48 PDT)
- RE: Tleap-metalloprotein (Thu Apr 10 2003 - 19:42:53 PDT)
- RE: Trying to understand parm99.dat (Tue Apr 08 2003 - 18:48:48 PDT)
Youyi Peng
- Re: job stopped (Thu Apr 24 2003 - 13:33:37 PDT)
- Re: job stopped (Thu Apr 24 2003 - 11:49:47 PDT)
- job stopped (Thu Apr 24 2003 - 10:52:12 PDT)
- Re: MD went crazy (Fri Apr 18 2003 - 12:28:14 PDT)
- Re: MD went crazy (Fri Apr 18 2003 - 11:55:51 PDT)
- Re: MD went crazy (Fri Apr 18 2003 - 11:33:26 PDT)
- Re: MD went crazy (Fri Apr 18 2003 - 10:36:35 PDT)
- Re: MD went crazy (Fri Apr 18 2003 - 09:17:24 PDT)
- MD went crazy (Fri Apr 18 2003 - 08:20:25 PDT)
- makeDIST_RST (Wed Apr 16 2003 - 19:24:19 PDT)
- CYS and HIS (Wed Apr 16 2003 - 07:20:40 PDT)
- ambpdb (Tue Apr 15 2003 - 18:32:22 PDT)
- ibelly and ntr (Tue Apr 15 2003 - 14:59:59 PDT)
yuan bo
- leap problem (Wed Apr 23 2003 - 20:49:36 PDT)
- diffusion coefficients (Sun Apr 13 2003 - 19:34:25 PDT)
yuann
- A problem in Sander production dynamics (Mon Apr 14 2003 - 01:37:50 PDT)
- Problem of Hbond in CARNAL (Tue Apr 01 2003 - 04:08:59 PST)
Yuhui Cheng
- A weird antechamber error (Tue Apr 01 2003 - 20:21:46 PST)
Yunfeng Hu
- id_torus(): Could not find torus for atoms 1878 and 1894 (Mon Apr 14 2003 - 15:26:18 PDT)
Yuuki Komata
- atom position restraints (Tue Apr 29 2003 - 18:34:06 PDT)
- atom position restraints (Tue Apr 29 2003 - 05:44:25 PDT)

Amber Archive Apr 2003 by author